Understanding the "Rules of Engagement" for Membrane Protein Folding. Ph.D
- Characterising the structural and energetic properties in helical-packing of de novo transmembrane helical peptides using a combination of Molecular Dynamics, Biophysics and Molecular Biology. Dimer affinity is determined in vivo using TOXCAT assays.
- Exploring novel potential mean force calculations to help understand how key mutations in a transmembrane peptides effect their ability to form dimers.
- Using coarse-grained simulations to explore the clustering of many transmembrane peptides.
This is a joint Ph.D project with my supervisors, Rebecca Notman from CSC (based in the Theoretical and Computational Chemistry department) and Ann Dixon from Chemical Biology. The project is funded by the EPSRC.
- Elucidating protein secondary structure with circular dichroism and a self organising map neural network. Vincent Hall, Anthony Nash, Evor Hines, Alison Rodger. (Awaiting submission).
- Effects of the oncogenic V664E mutation on membrane insertion, structure, and interactions of the Neu transmembrane domain: Mechanistic insights revealed from biophysical analyses and molecular dynamics simulation. Andrew J. Beevers, Anthony Nash, Martha Salazar-Cancino, David J. Scott, Rebecca Notman, Ann M. Dixon. Biochemistry. (Mar 2012).
- A Framework Proposition for Cellular Locality of Dictyostelium Modelled in Pi-Calculus. Anthony Nash and Sara Kalvala. CoSMoS, 2009.
|Single neu peptide embedded in a fully solvated POPC bilayer. 2012.||A fragment from an automaton encoded using Pi-Calculus. The system models cAMP signals. 2009.|
Education - MSc, MSc, BSc. Hons
Mathematical Biology and Biophysical Chemistry MSc (2009-2010) - Warwick
Included modules on mathematical biology, numerical analysis, molecular simulations, statistics and bioinformatics, microscopy, spectroscopy, and regulatory networks. My computational mini project focused on developing a model of spatial predator-prey dynamics in a Myxobacteria colony using a membrane-computing framework (P-Systems). This was accepted for publication in the 2010 CoSMoS conference preceedings. During my biophysics project I helped characterise the secondary structure and structural dynamics of Methanethiol Oxidase using circular dichroism. For my final project I was based at HRI under the supervision of Dr Hendrik Schäfef. I successfully purified methanethiol oxidase from Methylophaga thiooxidans using HPLC, gas chromotography and a formaldehyde colormetric assay.
Natural Computation MSc (2003-2004) - Birmingham
Modules included evolutionary algorithms, neural computation, DNA computing and Quantum Computing. My miniprojects focused on evolutionary algorithms in predator-prey cellular automata simulations and messy genetic algorithms for L-System design and evolutionary autocatalytic networks.
Artificial Intelligence BSc. Hons (1998-2002) - Birmingham
Genetic algortihms, neural networks and traditional artificial intelligence. Software design, UML, formal methods, discrete mathematics and logic.
Employement - Professional Software Engineer
Between 2004 and 2010 I was working as a qualified software engineer for the mobile devices industry, I was an engineer in a small team developing customisation software (patent number: US 2006/0167577 A1). My 5-6 years in private industry taught me punctual time managent, professional leadership and negotiation skills, software lifecycle and deliveries, and a myriad of technical design/engineer skills (as listed below). I strongly believe that my vocational experience has and will continue to benefit my PhD studies.
Motorola Mobile Devices - Software Engineer (2005-2009)
Java J2EE/J2SE software engineer, with experience in C/C++ build environments, distributed computing, object orientated design, UML, and managing a team of contractors. Was a member of the R&D team who developed the Motorola Z8, Z10 and Z12.
- Java (J2SE/J2EE)
- Clearcase (Software Repository)
Sendo - Software Engineer (2004-2005)
Was a member of the R&D team who developed the Sendo X and Sendo X2.
- Java J2SE.
- Clearcase (Software Repository)